-## DNA.R (2008-01-19)
+## DNA.R (2008-02-08)
## Manipulations and Comparisons of DNA Sequences
if (is.list(x)) x <- unlist(x)
n <- length(x)
BF <- .C("BaseProportion", as.raw(x), as.integer(n),
- double(4), PACKAGE = "ape")[[3]]
+ double(4), DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")[[3]]
names(BF) <- letters[c(1, 3, 7, 20)]
BF
}
s <- n[2]
n <- n[1]
ans <- .C("SegSites", x, as.integer(n), as.integer(s),
- integer(s), PACKAGE = "ape")
+ integer(s), DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
which(as.logical(ans[[4]]))
}
ans <- sum(dist.dna(x, "raw", pairwise.deletion = pairwise.deletion))/
(n*(n - 1)/2)
if (variance) {
- var <- (n + 1)*ans/(3*(n + 1)*s) + 2*(n^2 + n + 3)*ans/(9*n*(n - 1))
+ var <- (n + 1)*ans/(3*(n + 1)*dim(x)[2]) + 2*(n^2 + n + 3)*ans/(9*n*(n - 1))
ans <- c(ans, var)
}
ans
d <- .C("dist_dna", x, as.integer(n), as.integer(s),
as.integer(imod), double(Ndist), BF,
as.integer(pairwise.deletion), as.integer(variance),
- var, as.integer(gamma), alpha, PACKAGE = "ape")
+ var, as.integer(gamma), alpha, DUP = FALSE, NAOK = TRUE,
+ PACKAGE = "ape")
if (variance) var <- d[[9]]
d <- d[[5]]
if (imod == 11) {